lib/CXGN/Cview/Map_overviews/Individual.pm

   1
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::Map_overviews::Individual - a class to display genetic map overviews associated with individual that contain chromosome fragments from other accessions (such as ILs) or carry genes mapped between 2 flanking markers.
   6
   7 =head1 SYNOPSYS
   8
   9
  10 =head1 DESCRIPTION
  11
  12
  13 =head1 AUTHOR(S)
  14
  15 Lukas Mueller (lam87@cornell.edu)
  16
  17 =head1 VERSION
  18
  19
  20 =head1 LICENSE
  21
  22
  23 =head1 FUNCTIONS
  24
  25 This class implements the following functions:
  26
  27 =cut
  28
  29 use strict;
  30 #use CXGN::Map::IndividualMap;
  31
  32 package CXGN::Cview::Map_overviews::Individual;
  33
  34 use CXGN::Cview::Map_overviews;
  35
  36 use base qw | CXGN::Cview::Map_overviews |;
  37
  38 =head2 function new
  39
  40   Synopsis:
  41   Arguments:
  42   Returns:
  43   Side effects:
  44   Description:
  45
  46 =cut
  47
  48 sub new {
  49     my $class = shift;
  50
  51     my $self = $class->SUPER::new(@_);
  52     my $individual_id = shift;
  53     $self->set_individual_id($individual_id);
  54     $self->render_map();
  55     if (!$self->get_cache()->is_valid() && !$self->get_chromosome_count()) {
  56         return undef;
  57     }
  58     return $self;
  59 }
  60
  61 =head2 accessors set_individual_id, get_individual_id
  62
  63   Property:
  64   Setter Args:
  65   Getter Args:
  66   Getter Ret:
  67   Side Effects:
  68   Description:
  69
  70 =cut
  71
  72 sub get_individual_id {
  73     my $self=shift;
  74     return $self->{individual_id};
  75 }
  76
  77 sub set_individual_id {
  78     my $self=shift;
  79     $self->{individual_id}=shift;
  80 }
  81
  82
  83 =head2 function render_map
  84
  85   Synopsis:
  86   Arguments:
  87   Returns:
  88   Side effects:
  89   Description:
  90   To Do: move this to the data adapter
  91
  92 =cut
  93
  94 sub render_map {
  95     my $self = shift;
  96     my $individual_id = $self->get_individual_id();
  97
  98     #$self->get_cache()->set_force(1); # during development
  99     $self->get_cache()->set_key("individual overview $individual_id");
 100     $self->get_cache()->set_expiration_time(); # should never expire...
 101     $self->get_cache()->set_map_name("overview");
 102
 103     if ($self->get_cache()->is_valid()) { return; }
 104
 105     my $IMAGE_WIDTH = 700;
 106
 107     # get chromosome number of the individual in question.
 108     my $chr_q = "SELECT count(distinct(linkage_group.lg_name)) FROM phenome.genotype
 109                  JOIN phenome.genotype_experiment using (genotype_experiment_id)
 110                  JOIN sgn.map_version ON (genotype_experiment.reference_map_id=sgn.map_version.map_id)
 111                  JOIN sgn.linkage_group using (map_version_id)
 112                  WHERE map_version.current_version='t' AND individual_id=?";
 113     my $chr_h = $self->prepare($chr_q);
 114     $chr_h->execute($individual_id);
 115     my ($chr_count) = $chr_h->fetchrow_array();
 116
 117     print STDERR "Individual has $chr_count chromosomes.\n";
 118     $self->set_chromosome_count($chr_count);
 119     if (!$chr_count) { return; }
 120
 121     $self->set_horizontal_spacing( int($IMAGE_WIDTH/($chr_count+1)) );
 122
 123     my %lengths = ();
 124
 125     my $query = "SELECT lg_name, max(position), map_version.map_id FROM sgn.linkage_group
 126                    JOIN sgn.marker_location using (lg_id)
 127                    JOIN sgn.map_version on (map_version.map_version_id=linkage_group.map_version_id)
 128                    JOIN phenome.genotype_experiment on (map_version.map_id=genotype_experiment.reference_map_id)
 129                    JOIN phenome.genotype using (genotype_experiment_id)
 130                    WHERE genotype.individual_id=?
 131                          AND map_version.current_version='t'
 132                    GROUP BY lg_name, map_version.map_id";
 133
 134     print STDERR "QUERY: $query\n";
 135
 136     my $sth = $self->prepare($query);
 137     $sth ->execute($self->get_individual_id());
 138     my $map_id = 0;
 139     while (my ($lg_name, $length, $reference_map_id) = $sth->fetchrow_array()) {
 140         print STDERR "LENGTHS: $lg_name is $length long.\n";
 141         $lengths{$lg_name}=$length;
 142         $map_id=$reference_map_id;
 143     }
 144
 145
 146
 147     my @c = ();
 148 #    my %clen = $self->get_map()->get_linkage_group_lengths();
 149     $self->{map_image}=CXGN::Cview::MapImage->new("", 700, 200);
 150     foreach my $chr (0..($chr_count-1)) {
 151         print STDERR "Generating chromosome $chr...\n";
 152         $c[$chr] = CXGN::Cview::Chromosome->new();
 153         $c[$chr]->set_vertical_offset(40);
 154         $c[$chr]->set_width(12);
 155         $c[$chr]->set_height(100);
 156         $c[$chr]->set_caption($chr+1);
 157         $c[$chr]->set_length($lengths{$chr+1});
 158         $c[$chr]->set_horizontal_offset(($chr+1) * $self->get_horizontal_spacing());
 159         $c[$chr]->set_hilite_color(100, 100, 200);
 160
 161         $self->{map_image}->add_chromosome($c[$chr]);
 162     }
 163
 164     # now get the fragments to be highlighted
 165     #
 166     my $query2 = "SELECT linkage_group.lg_name, position, type, zygocity_code FROM phenome.genotype
 167                  JOIN phenome.genotype_region USING(genotype_id)
 168                  JOIN phenome.genotype_experiment USING (genotype_experiment_id)
 169                  JOIN sgn.map_version ON (genotype_experiment.reference_map_id=sgn.map_version.map_id)
 170                  JOIN sgn.marker_location using(map_version_id)
 171                  JOIN sgn.marker_experiment using(location_id)
 172                  JOIN sgn.linkage_group ON (genotype_region.lg_id=linkage_group.lg_id)
 173                  WHERE map_version.current_version='t'
 174                    AND genotype_region.marker_id_ns=sgn.marker_experiment.marker_id
 175                  AND individual_id =? and genotype_experiment.preferred='t' ORDER BY position";
 176
 177  #   print STDERR "QUERY2: $query2\n";
 178
 179
 180     my $query3 = "SELECT linkage_group.lg_name, position  FROM phenome.genotype
 181                  JOIN phenome.genotype_region USING(genotype_id)
 182                  JOIN phenome.genotype_experiment USING (genotype_experiment_id)
 183                  JOIN sgn.map_version ON (genotype_experiment.reference_map_id=sgn.map_version.map_id)
 184                  JOIN sgn.marker_location using(map_version_id)
 185                  JOIN sgn.marker_experiment using(location_id)
 186                  JOIN sgn.linkage_group ON (genotype_region.lg_id=linkage_group.lg_id)
 187                  WHERE map_version.current_version='t'
 188                    -- AND phenome.genotype_region.lg_id=sgn.linkage_group.lg_id
 189                    AND marker_id_sn=sgn.marker_experiment.marker_id
 190                  AND individual_id =? and genotype_experiment.preferred='t' ORDER BY position";
 191
 192 #    print STDERR "QUERY3: $query3\n";
 193
 194     my $sth2 = $self-> prepare($query2);
 195     $sth2->execute($individual_id);
 196
 197     my $sth3 = $self-> prepare($query3);
 198     $sth3->execute($individual_id);
 199
 200     while (my ($chr1, $top_marker, $type, $zygocity_code) = $sth2->fetchrow_array()) {
 201         my ($chr2, $bottom_marker) = $sth3->fetchrow_array();
 202
 203         if ($type eq "map") {
 204             my $m = CXGN::Cview::Marker->new($c[$chr1-1]);
 205             $m->get_label()->set_hidden(1);
 206
 207             my @color = (200, 200, 200);
 208             if ($zygocity_code eq "a") { @color = (255, 0, 0); }
 209             if ($zygocity_code eq "b") { @color = (0, 0, 255); }
 210             if ($zygocity_code eq "c") { @color = (200, 100, 0); }
 211             if ($zygocity_code eq "d") { @color = (0, 100, 200); }
 212             if ($zygocity_code eq "h") { @color = (50, 50, 50); }
 213             $m->set_color(@color);
 214             $m->set_offset($top_marker);
 215             $c[$chr1-1]->add_marker($m);
 216             $c[$chr1-1]->set_url("/cview/view_chromosome.pl?chr_nr=$chr1&amp;map_id=$map_id&amp;show_ruler=1");
 217         }
 218
 219         elsif ("$chr1" eq "$chr2") {
 220
 221             my $m = CXGN::Cview::Marker::RangeMarker->new($c[$chr1-1]);
 222             #$m->get_label()->set_stacking_level(1);
 223 #           $m->set_label_side("right");
 224             $m->get_label()->set_name("IL");
 225
 226             my $offset = ($top_marker+$bottom_marker)/2;
 227             $m->set_offset($offset);
 228             $m->set_north_range($offset-$top_marker);
 229             $m->set_south_range($bottom_marker-$offset);
 230
 231             $c[$chr1-1]->add_marker($m);
 232             $m->set_hilite_chr_region(1);
 233             #$m->get_label()->set_url("/cview/view_chromosome.pl?map_id=5&cM_start=$top_marker&cM_end=$bottom_marker&show_zoomed=1");
 234             $c[$chr1-1]->set_url("/cview/view_chromosome.pl?chr_nr=$chr1&amp;map_id=$map_id&amp;cM_start=".($top_marker-1)."&amp;cM_end=".($bottom_marker+1)."&amp;show_zoomed=1&amp;show_ruler=1");
 235
 236             #print STDERR "Fragment: $offset, $top_marker, $bottom_marker\n";
 237         }
 238         else { print STDERR "[Individual_overviews] $chr1 should be the same as $chr2...\n"; }
 239
 240     }
 241     $self->get_cache()->set_image_data( $self->{map_image}->render_png_string() );
 242     $self->get_cache()->set_image_map_data( $self->{map_image}->get_image_map("overview") );
 243
 244 }
 245
 246 =head2 function get_cache_key
 247
 248   Synopsis:
 249   Arguments:
 250   Returns:
 251   Side effects:
 252   Description:
 253
 254 =cut
 255
 256 sub get_cache_key {
 257     my $self = shift;
 258     return "Individual".$self->get_individual_id();
 259 }
 260
 261
 262 =head2 accessors set_chromosome_count, get_chromosome_count
 263
 264   Property:
 265   Setter Args:
 266   Getter Args:
 267   Getter Ret:
 268   Side Effects:
 269   Description:
 270
 271 =cut
 272
 273 sub get_chromosome_count {
 274     my $self=shift;
 275     return $self->{chromosome_count};
 276 }
 277
 278 sub set_chromosome_count {
 279     my $self=shift;
 280     $self->{chromosome_count}=shift;
 281 }
 282
 283
 284 package CXGN::Cview::Map_overviews::Individual_overview;
 285
 286 use base qw | CXGN::Cview::Map_overviews::Individual |;
 287
 288 sub new {
 289     my $class = shift;
 290     my $self = $class->SUPER::new(@_);
 291     return $self;
 292 }
 293
 294 return 1;